Align phosphate acetyltransferase; EC 2.3.1.8 (characterized)
to candidate WP_035702808.1 BA79_RS11095 phosphate butyryltransferase
Query= CharProtDB::CH_090885 (294 letters) >NCBI__GCF_000691145.1:WP_035702808.1 Length = 297 Score = 237 bits (605), Expect = 2e-67 Identities = 124/287 (43%), Positives = 187/287 (65%), Gaps = 3/287 (1%) Query: 6 LVEMARGKGKKLAVAAANDDHVIEAVYRAWRERVCEPVLFGPEEEITRIIE--ELVPEWK 63 +++ ++ + K AVA A D+ V+ A+ A +V +L G + + +++ E+ +W Sbjct: 7 IIKASQLQNKTAAVAHAEDEEVLHAIKMAIERKVARFLLVGNKRNLKELVKQHEINEDWI 66 Query: 64 NPQIIDCPPEEAGRLAVEAVSKGECDFLMKGKIKTGDLMKIYLDERYGLRTGKTMAMVSV 123 + D P EE+ ++AV+AVS+ D LMKG + T L+K L++ YGLRT ++ V+ Sbjct: 67 DIIHSDSP-EESAKIAVQAVSENHADILMKGHVPTAILLKAVLNKEYGLRTASVLSHVAA 125 Query: 124 MEIPDFPRPLIISDPGMLISPTLEQKVDMIEHCVRVANVMGLETPKVAVVGAIEVVNPKM 183 E+P F R + ++D M I+P L ++ + V+VA +G + PKVAV+ A+EVVNP M Sbjct: 126 FEVPGFDRFIYVTDSAMNIAPDLNMLKEITVNSVQVAQAVGNDMPKVAVLSAVEVVNPAM 185 Query: 184 PITMEAAILSKMNQRGQIKGCIVDGPFALDNVVSEEAAKKKGIQSPVAGKADILILPDIE 243 T+ AA L++MN+RGQI GC++DGP ALDN +S+ AA K I S VAG ADIL++P IE Sbjct: 186 DSTLTAASLAQMNRRGQISGCLIDGPLALDNAISQTAASHKNITSDVAGHADILLVPTIE 245 Query: 244 AANILYKALVFLAKAKSASTILGGKVPVVLTSRADSEETKFYSIALS 290 A NILYK+L++ A AK + + G K P+ LTSR+DS E+K YSIAL+ Sbjct: 246 AGNILYKSLIYFAHAKVGAVVAGAKAPIALTSRSDSAESKLYSIALA 292 Lambda K H 0.319 0.136 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 190 Number of extensions: 6 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 294 Length of database: 297 Length adjustment: 26 Effective length of query: 268 Effective length of database: 271 Effective search space: 72628 Effective search space used: 72628 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory